MRE11 - SULSO - GREMLIN Contacts

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MRE11 - DNA double-strand break repair protein Mre11

UniProt:	Q97WG9	Sequences: MVQILHISDTHLGKRQYSLVEREKDIYDIFSQLVDIAIKEHVDVIIHSGDLFDVSSPTTNALVMAIKILKRLKDVNIPFLSIPGDHDTPKRKGYLIPHNILSELDLIKILNYEKPYIIKGIEVYGIPHIPTVSKSILVSALSALRPKSSRSILLLHQGVKQILPYDGSWQMELGSLPKGFGYYALGHIHTRWRLTQDDGSVIAIAGSPDIMREEEIEGYEKFGKGAYLIDFSKDLPILSTINITVRPQKVVTINTKNIKKDILTIRDDLIEHNKSENNKPILHIIVEGERMRKDLLYKELLPLNDVALYYRIYKDETTQTVDNLSYTLPRDKGLDKIIIEYLTKYEKFSEDEANLILQMIKNVESDEIVNEILKKLTGVNL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	381 (339)
Sequences:	4067 (3248)
Seq/√Len:	176.4

ECOLI - SBCD
BACSU - SBCD YHAO
HALSA - MRE11
SULSO - MRE11

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
46_I	154_L	5.136	1.00
40_E	239_S	4.113	1.00
225_G	240_T	3.885	1.00
36_I	226_A	3.762	1.00
5_L	42_V	3.472	1.00
42_V	228_L	3.314	1.00
3_Q	230_D	3.262	1.00
40_E	241_I	3.257	1.00
223_G	242_N	3.145	1.00
4_I	44_V	3.132	1.00
33_L	208_P	3.040	1.00
37_A	45_I	3.003	1.00
80_L	123_V	2.789	1.00
31_S	71_R	2.775	1.00
228_L	241_I	2.767	1.00
7_I	47_H	2.728	1.00
35_D	39_K	2.614	1.00
227_Y	238_L	2.611	1.00
36_I	241_I	2.557	1.00
36_I	40_E	2.505	1.00
65_A	69_L	2.445	1.00
8_S	205_A	2.436	1.00
203_A	227_Y	2.433	1.00
122_E	149_S	2.345	1.00
230_D	239_S	2.314	1.00
252_T	285_I	2.291	1.00
7_I	10_T	2.255	1.00
38_I	75_V	2.177	1.00
48_S	154_L	2.176	1.00
40_E	228_L	2.148	1.00
4_I	229_I	2.118	1.00
250_V	283_H	2.095	1.00
193_R	200_S	2.073	1.00
6_H	184_A	2.020	1.00
250_V	285_I	1.996	1.00
30_F	68_I	1.988	1.00
117_I	122_E	1.984	1.00
44_V	80_L	1.965	1.00
44_V	123_V	1.920	1.00
230_D	237_I	1.915	1.00
46_I	123_V	1.880	1.00
252_T	287_E	1.848	1.00
249_K	280_P	1.840	1.00
231_F	236_P	1.834	1.00
31_S	68_I	1.834	1.00
153_L	180_F	1.825	1.00
162_I	188_I	1.804	1.00
191_R	227_Y	1.769	1.00
216_I	250_V	1.754	1.00
333_G	336_K	1.723	1.00
37_A	77_I	1.712	1.00
7_I	33_L	1.708	1.00
123_V	152_I	1.688	1.00
27_Y	64_M	1.674	1.00
349_S	352_E	1.669	1.00
12_L	65_A	1.660	1.00
213_E	283_H	1.659	1.00
35_D	71_R	1.654	1.00
25_D	246_R	1.646	1.00
22_R	25_D	1.641	1.00
6_H	182_Y	1.632	1.00
29_I	33_L	1.612	1.00
37_A	42_V	1.600	1.00
227_Y	240_T	1.598	1.00
226_A	243_I	1.598	1.00
10_T	47_H	1.593	1.00
29_I	208_P	1.592	1.00
120_G	150_R	1.582	1.00
153_L	183_Y	1.579	1.00
5_L	37_A	1.554	1.00
31_S	35_D	1.548	1.00
8_S	48_S	1.545	1.00
37_A	72_L	1.542	1.00
5_L	228_L	1.513	1.00
33_L	226_A	1.512	1.00
122_E	151_S	1.494	1.00
191_R	225_G	1.492	1.00
24_K	28_D	1.487	1.00
5_L	226_A	1.484	1.00
357_L	361_K	1.458	1.00
299_E	302_P	1.455	1.00
80_L	125_G	1.454	1.00
350_E	353_A	1.452	1.00
3_Q	40_E	1.451	1.00
51_L	81_S	1.449	1.00
183_Y	202_I	1.448	1.00
254_N	257_N	1.445	1.00
138_V	141_L	1.441	1.00
121_I	152_I	1.437	1.00
354_N	358_Q	1.409	1.00
38_I	71_R	1.398	1.00
64_M	68_I	1.395	1.00
123_V	154_L	1.392	1.00
51_L	65_A	1.387	1.00
16_Q	22_R	1.383	1.00
210_I	247_P	1.376	1.00
203_A	238_L	1.373	1.00
14_K	211_M	1.358	1.00
2_V	230_D	1.334	1.00
356_I	360_I	1.325	1.00
229_I	238_L	1.323	1.00
330_R	333_G	1.319	1.00
115_P	118_I	1.307	1.00
25_D	281_I	1.305	1.00
191_R	240_T	1.304	1.00
35_D	38_I	1.288	1.00
82_I	154_L	1.286	1.00
294_D	298_K	1.280	1.00
150_R	231_F	1.277	1.00
135_S	138_V	1.270	1.00
124_Y	180_F	1.266	1.00
232_S	235_L	1.256	1.00
300_L	303_L	1.251	1.00
32_Q	35_D	1.250	1.00
180_F	183_Y	1.241	1.00
5_L	36_I	1.235	1.00
26_I	211_M	1.225	1.00
252_T	313_Y	1.222	1.00
146_P	149_S	1.221	1.00
36_I	39_K	1.215	1.00
71_R	74_D	1.199	1.00
124_Y	151_S	1.198	1.00
58_T	61_A	1.189	1.00
29_I	243_I	1.179	1.00
10_T	51_L	1.170	1.00
50_D	86_H	1.166	1.00
207_S	211_M	1.161	1.00
47_H	79_F	1.152	1.00
28_D	245_V	1.137	1.00
336_K	339_I	1.132	1.00
358_Q	362_N	1.124	1.00
350_E	354_N	1.121	1.00
28_D	31_S	1.120	1.00
14_K	53_D	1.112	1.00
334_L	339_I	1.105	1.00
34_V	68_I	1.103	1.00
69_L	79_F	1.099	1.00
27_Y	31_S	1.096	1.00
247_P	280_P	1.095	1.00
348_F	352_E	1.090	1.00
174_G	177_P	1.083	1.00
170_Q	173_L	1.082	1.00
337_I	340_E	1.079	1.00
105_D	108_K	1.075	1.00
6_H	185_L	1.074	1.00
29_I	209_D	1.060	1.00
135_S	141_L	1.050	1.00
38_I	77_I	1.042	1.00
251_V	284_I	1.037	0.99
121_I	150_R	1.037	0.99
191_R	203_A	1.036	0.99
44_V	152_I	1.035	0.99
352_E	356_I	1.032	0.99
117_I	120_G	1.030	0.99
254_N	287_E	1.027	0.99
32_Q	244_T	1.027	0.99
297_Y	301_L	1.026	0.99
34_V	72_L	1.023	0.99
339_I	342_L	1.020	0.99
349_S	353_A	1.009	0.99
32_Q	243_I	1.004	0.99
334_L	338_I	1.001	0.99
53_D	211_M	1.001	0.99
97_P	101_L	0.993	0.99
190_T	222_F	0.989	0.99
27_Y	67_K	0.984	0.99
353_A	357_L	0.977	0.99
4_I	46_I	0.977	0.99
337_I	341_Y	0.973	0.99
229_I	236_P	0.971	0.99
78_P	107_I	0.969	0.99
207_S	224_K	0.969	0.99
165_Y	168_S	0.967	0.99
137_L	140_A	0.967	0.99
348_F	356_I	0.964	0.99
168_S	171_M	0.962	0.99
46_I	152_I	0.959	0.99
331_D	334_L	0.959	0.99
193_R	203_A	0.958	0.99
151_S	181_G	0.954	0.99
352_E	360_I	0.940	0.99
194_L	198_D	0.940	0.99
125_G	154_L	0.939	0.99
115_P	122_E	0.938	0.99
168_S	172_E	0.934	0.99
68_I	71_R	0.929	0.99
348_F	360_I	0.928	0.99
167_G	171_M	0.927	0.99
86_H	189_H	0.923	0.99
23_E	60_N	0.920	0.99
25_D	209_D	0.919	0.99
142_S	180_F	0.919	0.99
335_D	342_L	0.918	0.99
159_V	194_L	0.917	0.99
253_I	257_N	0.913	0.99
142_S	179_G	0.911	0.99
50_D	85_D	0.910	0.99
3_Q	228_L	0.908	0.99
46_I	229_I	0.905	0.99
83_P	127_P	0.899	0.99
332_K	340_E	0.895	0.98
296_L	302_P	0.894	0.98
65_A	81_S	0.891	0.98
58_T	62_L	0.889	0.98
13_G	61_A	0.887	0.98
283_H	309_Y	0.885	0.98
66_I	99_N	0.885	0.98
299_E	303_L	0.880	0.98
339_I	343_T	0.877	0.98
213_E	248_Q	0.876	0.98
182_Y	203_A	0.872	0.98
94_Y	97_P	0.869	0.98
296_L	299_E	0.867	0.98
228_L	239_S	0.866	0.98
6_H	205_A	0.862	0.98
155_L	185_L	0.862	0.98
50_D	189_H	0.860	0.98
108_K	111_N	0.858	0.98
285_I	311_R	0.850	0.98
111_N	114_K	0.849	0.98
255_T	292_R	0.849	0.98
46_I	184_A	0.847	0.98
34_V	75_V	0.846	0.98
38_I	74_D	0.843	0.98
173_L	202_I	0.839	0.98
359_M	362_N	0.836	0.98
72_L	79_F	0.834	0.98
109_I	125_G	0.830	0.98
285_I	313_Y	0.828	0.98
298_K	301_L	0.827	0.97
335_D	339_I	0.823	0.97
330_R	339_I	0.817	0.97
44_V	121_I	0.816	0.97
210_I	224_K	0.813	0.97
156_H	187_H	0.812	0.97
83_P	89_P	0.809	0.97
45_I	79_F	0.807	0.97
4_I	121_I	0.806	0.97
16_Q	248_Q	0.803	0.97
355_L	360_I	0.801	0.97
226_A	241_I	0.793	0.97
70_K	74_D	0.792	0.97
52_F	65_A	0.782	0.96
216_I	222_F	0.782	0.96
48_S	205_A	0.781	0.96
13_G	57_P	0.779	0.96
152_I	229_I	0.778	0.96
357_L	362_N	0.778	0.96
126_I	137_L	0.774	0.96
83_P	110_L	0.773	0.96
104_L	107_I	0.771	0.96
81_S	108_K	0.767	0.96
184_A	203_A	0.762	0.96
130_P	133_S	0.761	0.96
42_V	45_I	0.759	0.96
337_I	342_L	0.755	0.96
39_K	241_I	0.755	0.96
33_L	37_A	0.754	0.96
343_T	347_K	0.753	0.96
332_K	335_D	0.753	0.96
7_I	208_P	0.751	0.96
358_Q	361_K	0.748	0.95
126_I	155_L	0.745	0.95
53_D	224_K	0.744	0.95
86_H	156_H	0.744	0.95
307_A	310_Y	0.742	0.95
65_A	94_Y	0.736	0.95
11_H	189_H	0.734	0.95
63_V	102_S	0.734	0.95
340_E	343_T	0.730	0.95
348_F	353_A	0.730	0.95
339_I	353_A	0.728	0.95
135_S	139_S	0.727	0.95
333_G	341_Y	0.727	0.95
88_T	131_T	0.726	0.95
27_Y	71_R	0.726	0.95
150_R	181_G	0.722	0.95
336_K	353_A	0.721	0.94
297_Y	300_L	0.721	0.94
36_I	228_L	0.720	0.94
48_S	82_I	0.718	0.94
59_T	62_L	0.717	0.94
81_S	106_L	0.716	0.94
325_S	328_L	0.715	0.94
332_K	336_K	0.713	0.94
73_K	106_L	0.711	0.94
275_S	278_N	0.711	0.94
32_Q	245_V	0.711	0.94
5_L	45_I	0.710	0.94
176_L	183_Y	0.709	0.94
217_E	223_G	0.707	0.94
29_I	244_T	0.706	0.94
69_L	106_L	0.705	0.94
104_L	108_K	0.705	0.94
48_S	69_L	0.703	0.94
12_L	30_F	0.701	0.94
333_G	342_L	0.698	0.93
85_D	189_H	0.698	0.93
347_K	352_E	0.697	0.93
334_L	342_L	0.696	0.93
25_D	28_D	0.695	0.93
208_P	243_I	0.694	0.93
80_L	116_Y	0.690	0.93
115_P	119_K	0.690	0.93
145_R	151_S	0.686	0.93
4_I	231_F	0.685	0.93
352_E	355_L	0.684	0.93
10_T	30_F	0.682	0.93
297_Y	307_A	0.681	0.93
208_P	226_A	0.681	0.93
328_L	332_K	0.680	0.93
330_R	334_L	0.679	0.93
10_T	208_P	0.679	0.93
71_R	75_V	0.677	0.92
355_L	358_Q	0.675	0.92
340_E	347_K	0.674	0.92
12_L	58_T	0.674	0.92
23_E	26_I	0.669	0.92
261_D	273_N	0.668	0.92
136_I	139_S	0.668	0.92
167_G	172_E	0.665	0.92
33_L	45_I	0.663	0.92
26_I	209_D	0.663	0.92
30_F	34_V	0.663	0.92
101_L	108_K	0.662	0.92
330_R	335_D	0.661	0.92
277_N	280_P	0.660	0.91
22_R	209_D	0.659	0.91
333_G	337_I	0.658	0.91
322_D	326_Y	0.657	0.91
43_D	119_K	0.656	0.91
329_P	336_K	0.656	0.91
346_E	349_S	0.656	0.91
100_I	104_L	0.656	0.91
331_D	339_I	0.653	0.91
52_F	97_P	0.652	0.91
115_P	124_Y	0.652	0.91
43_D	230_D	0.652	0.91
86_H	187_H	0.650	0.91
255_T	258_I	0.649	0.91
127_P	204_I	0.648	0.91
52_F	62_L	0.648	0.91
309_Y	313_Y	0.647	0.91
2_V	231_F	0.647	0.91
169_W	172_E	0.644	0.90
256_K	260_K	0.644	0.90
135_S	140_A	0.642	0.90
322_D	325_S	0.642	0.90
329_P	337_I	0.636	0.90
347_K	358_Q	0.635	0.90
349_S	354_N	0.634	0.90
310_Y	314_K	0.634	0.90
22_R	246_R	0.632	0.90
146_P	151_S	0.631	0.90
323_N	346_E	0.631	0.90
85_D	128_H	0.630	0.89
34_V	71_R	0.630	0.89
199_G	202_I	0.630	0.89
45_I	72_L	0.627	0.89
45_I	75_V	0.626	0.89
348_F	354_N	0.626	0.89
182_Y	229_I	0.625	0.89
48_S	184_A	0.624	0.89
346_E	352_E	0.623	0.89
24_K	27_Y	0.622	0.89
334_L	337_I	0.621	0.89
72_L	77_I	0.621	0.89
7_I	45_I	0.618	0.89
309_Y	312_I	0.617	0.89
333_G	339_I	0.616	0.88
73_K	102_S	0.613	0.88
73_K	105_D	0.613	0.88
13_G	23_E	0.612	0.88
63_V	67_K	0.612	0.88
16_Q	213_E	0.611	0.88
45_I	77_I	0.611	0.88
354_N	357_L	0.610	0.88
99_N	102_S	0.609	0.88
128_H	158_G	0.608	0.88
127_P	155_L	0.605	0.88
4_I	152_I	0.604	0.87
44_V	229_I	0.604	0.87
255_T	286_V	0.604	0.87
22_R	207_S	0.603	0.87
107_I	110_L	0.603	0.87
201_V	238_L	0.602	0.87
22_R	26_I	0.601	0.87
151_S	157_Q	0.600	0.87
33_L	42_V	0.599	0.87
169_W	173_L	0.599	0.87
8_S	184_A	0.598	0.87
45_I	68_I	0.597	0.87
166_D	170_Q	0.596	0.87
257_N	261_D	0.593	0.86
147_K	179_G	0.592	0.86
227_Y	230_D	0.592	0.86
341_Y	344_K	0.590	0.86
258_I	262_I	0.589	0.86
13_G	211_M	0.588	0.86
235_L	238_L	0.588	0.86
85_D	156_H	0.586	0.86
339_I	344_K	0.586	0.86
7_I	226_A	0.585	0.86
315_D	318_T	0.584	0.86
347_K	361_K	0.584	0.86
152_I	231_F	0.584	0.86
162_I	192_W	0.579	0.85
88_T	158_G	0.579	0.85
78_P	105_D	0.578	0.85
304_N	307_A	0.577	0.85
286_V	300_L	0.576	0.85
324_L	327_T	0.576	0.85
328_L	331_D	0.576	0.85
321_V	324_L	0.576	0.85
101_L	105_D	0.575	0.85
115_P	120_G	0.574	0.85
330_R	341_Y	0.573	0.85
355_L	359_M	0.572	0.84
207_S	212_R	0.571	0.84
11_H	187_H	0.571	0.84
185_L	204_I	0.570	0.84
335_D	356_I	0.566	0.84
246_R	306_V	0.565	0.84
225_G	243_I	0.564	0.84
350_E	360_I	0.563	0.84
108_K	112_Y	0.563	0.84
308_L	311_R	0.562	0.83
166_D	173_L	0.562	0.83
352_E	358_Q	0.561	0.83
110_L	113_E	0.560	0.83
47_H	81_S	0.560	0.83
323_N	326_Y	0.559	0.83
201_V	236_P	0.558	0.83
23_E	64_M	0.557	0.83
336_K	342_L	0.557	0.83
11_H	50_D	0.556	0.83
279_K	305_D	0.556	0.83
334_L	344_K	0.554	0.83
335_D	357_L	0.554	0.83
30_F	64_M	0.554	0.83
39_K	361_K	0.553	0.82
73_K	103_E	0.553	0.82
312_I	315_D	0.552	0.82
34_V	37_A	0.545	0.82
327_T	340_E	0.543	0.81
347_K	354_N	0.543	0.81
68_I	72_L	0.542	0.81
31_S	64_M	0.541	0.81
131_T	158_G	0.541	0.81
101_L	107_I	0.539	0.81
306_V	312_I	0.539	0.81
357_L	360_I	0.537	0.81
350_E	355_L	0.537	0.81
323_N	327_T	0.535	0.80
22_R	248_Q	0.535	0.80
348_F	351_D	0.534	0.80
47_H	51_L	0.533	0.80
85_D	187_H	0.533	0.80
53_D	92_K	0.532	0.80
232_S	237_I	0.531	0.80
313_Y	316_E	0.530	0.80
351_D	356_I	0.530	0.80
331_D	336_K	0.529	0.80
338_I	342_L	0.528	0.80
20_V	308_L	0.527	0.79
105_D	109_I	0.527	0.79
164_P	168_S	0.527	0.79
307_A	312_I	0.527	0.79
347_K	360_I	0.525	0.79
56_S	66_I	0.524	0.79
330_R	336_K	0.522	0.79
193_R	238_L	0.522	0.79
209_D	245_V	0.522	0.79
313_Y	317_T	0.520	0.78
338_I	341_Y	0.520	0.78
156_H	189_H	0.519	0.78
2_V	121_I	0.519	0.78
350_E	357_L	0.519	0.78
93_G	110_L	0.516	0.78
97_P	100_I	0.514	0.78
88_T	92_K	0.514	0.78
25_D	207_S	0.513	0.78
253_I	258_I	0.513	0.78
172_E	175_S	0.512	0.77
13_G	58_T	0.512	0.77
29_I	32_Q	0.511	0.77
315_D	319_Q	0.510	0.77
44_V	78_P	0.509	0.77
112_Y	134_K	0.509	0.77
341_Y	346_E	0.507	0.77
25_D	245_V	0.507	0.77
125_G	155_L	0.507	0.77
158_G	188_I	0.506	0.77
332_K	342_L	0.506	0.77
166_D	169_W	0.506	0.77
314_K	317_T	0.506	0.77
14_K	207_S	0.505	0.76
326_Y	329_P	0.505	0.76
308_L	312_I	0.505	0.76
146_P	350_E	0.505	0.76
12_L	27_Y	0.504	0.76
27_Y	61_A	0.504	0.76
10_T	33_L	0.504	0.76
329_P	340_E	0.504	0.76
26_I	207_S	0.501	0.76
57_P	88_T	0.500	0.76
336_K	340_E	0.500	0.76
305_D	309_Y	0.500	0.76

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
4ltyC	1	0.7769	100	0.399	Contact Map
3thoB	2	0.8793	100	0.408	Contact Map
1ii7A	2	0.7848	100	0.418	Contact Map
3av0A	1	0.9265	100	0.437	Contact Map
4nzvA	1	0.7585	100	0.454	Contact Map
4ykeA	2	0.7953	100	0.458	Contact Map
3t1iA	2	0.8478	100	0.482	Contact Map
4fbwA	2	0.7874	100	0.487	Contact Map
4fbkA	2	0.7979	100	0.492	Contact Map
2yvtA	1	0.5459	99.9	0.703	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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